Ruby / Sapphire

Early Game Titles

First image is from field_c102.ev, and second image is from saveflag.h.
The comments show "藍バージョン" and 朱バージョン", which could be translated as Indigo Version and Crimson Version.
There are also other possible translations for 朱, such as scarlet or vermillion. It is unknown whether Game Freak actually considered using these
as the titles, if they were abbreviations for the games, or if they were tentative titles to use until the names "Sapphire" and "Ruby" were decided on.
Thanks to KmiE_821 for helping with this.

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Early Evil Team Names

There are some mentions of マリン団 and トンネル団, or Team Marine and Team Tunnel in the source code.
These are likely early names for Team Aqua and Team Magma.

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Early Pokémon Names

Some Pokémon had different names early on. Most of these are from the file pokeyofs.h while Treecko's old name can be found in
several other files including opselect.c, message.c, message.h, ev_win.c, and r110_r0108.mes.

Pokemon	Early Name	Final Name (Japanese)	Notes
Treecko	ジュモリ (Jumori)	キモリ (Kimori)	from 樹 ju (trees) and 森 mori (forest)
Seedot	ダングリ (Danguri)	タネボー (Tanebō)	どんぐり donguri (acorn)
Breloom	グラッソー (Gurassō)	キノガッサ (Kinogassa)	possibly from grass and 草 sou (grass)?
Grumpig	ツイストン (Tsuisuton)	ブーピッグ (Būpiggu)	from twist and 豚 ton (pig)
Plusle	プラポ (Purapo)	プラスル (Purasuru)
Minun	マイラ (Maira)	マイナン (Mainan)
Altaria	アルタリス (Arutarisu)	チルタリス (Chirutarisu)	Closer to its final English name
Ralts	エクティ (Ekuti)	ラルトス (Rarutosu)
Metang	アイアング (Aiangu)	メタング (Metangu)	from iron
Jirachi	エリーム (Erīmu)	ジラーチ (Jirāchi)
Deoxys	ユニージェ (Yunīje)	デオキシス (Deokishisu)

Additionally, Flannery used to have a different name: アイリ (Airi).

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Unused in-game trades

Location: src_jp_final\source\koukan.def
There are 3 in-game trades that went unused in Ruby and Sapphire. Below is a table of them.

For the trades that did make it into the final game, the ability is set to either 0 or 1, which seems to correspond to one of the Pokémon's two abilities, but for the unused trades, the numbers are higher than 1. This could mean that at the time the trades were created, abilities were set using their index numbers instead of by a Pokémon's first/second ability. However, they are slightly off from the correct number. Walrein's ability is set to 48 (Early Bird), which is 1 off from 49 (Thick Fat) Duskull's is set to 23 (Shadow Tag) when it normally has 26 (Levitate). As for Seedot, 5 is nowhere near the correct number for its ability, which may mean that the order of abilities was shifted around during development.

Walrein's held item may also be an error. Just 1 slot behind Sharp Beak is the Mystic Water, which would probably be more fitting for a Walrein.

Location	Requested	Given	Nickname	IVs	Contest Stats	Ability	ID	Held Item	PV	OT	Sheen
Rustboro City			グリグリ (Guriguri)	4/4/4/4/4/4	10/10/10/10/10	5	22636	Great Ball	10000	ゲーフリ	10
Dewford Town			ウロウロ (Urouro)	4/4/4/4/4/4	10/10/10/10/10	26	22636	Bead Mail	20000	ゲーフリ	10
Sootopolis City			ブヨブヨ (Buyobuyo)	4/4/4/4/4/4	20/20/20/20/40 (High Toughness)	48	22636	Sharp Beak	30000	ゲーフリ	40

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Birch's Rewards

At one point, there were 162 Pokémon in the Hoenn Pokédex instead of the 202 that are in the final game. This included all newly introduced Gen III Pokémon except possibly Chimecho, and only 28 Pokémon returning from previous generations. In the final game, there are 67 returning Pokémon. It is not certain if they planned to leave it at 162 Pokémon or if it was just incomplete.

Professor Birch would congratulate the player for completing the Pokédex if they had 160 or more Pokémon. (Jirachi and Deoxys are not required)
Birch would also reward the player with different items depending on their progress with the Pokédex:
10+ Pokémon : Great Ball
30+ Pokémon : Exp. Share
50+ Pokémon : Dowsing Machine

In the final game, this does not happen, and the items are found elsewhere.

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The Berry Master's Neighbor

The Berry Master on Route 123 used to have a neighbor. There was an old man who would ask to see a certain Pokémon and reward the player if it was big enough. Two NPCs with the same function exists in the final game, but they are in Sootopolis city. Next to the Berry Master's house, there is no longer a second house, and a small lake takes its place.

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Berry Mechanics - Light & Temperature

It was planned to have the environment affect the growth of berries, with factors like light exposure and temperature.
You also would have been able to plant berries in more places, including caves and houses.

There are 5 categories of temperatures. They are determined by both the type of map and the weather.
If the temperature of the environment matches the berry’s ideal temperature, the growth time will be ¼ of the normal time.
If they do not match, the growth time will be doubled (making it slower), and the light exposure check will not be performed.

Similarly to the temperature, if the berry is exposed to the right amount of light, growth time will be reduced by ¼.
The details for each individual berry can be found in ポケモン_ﾙﾋﾞｰ･ｻﾌｧｲｱ\ポケモン_ﾙﾋﾞｰ･ｻﾌｧｲｱ\タネ仕様/タネのデータ011102.xls

Temperature	Location	Weather
Hot	Town, city, road	Harsh sunlight
Cold	Sea, water, ice	Ash, rain, thunder, mist, snow
Normal	Anything other than the above two
Hot or Normal	Hot or Normal
Cold or Normal	Cold or Normal

Light level	Location
TOWN	Town, city, road, cave, water, sea, ice, room
TCR	Town, city, road
TC	Town, city

Diamond / Pearl

Obtaining the Alarm Clock and Stopwatch Poketch Apps

It is already known that these two apps went unused, but not how they were meant to be obtained. It has been assumed that they were intended to be distributed at an event, but there is a script in the game to obtain them. In Pal Park, there is a girl who will give you Poketch apps if you show her certain Pokémon. She exists in the final game, but the player can only receive the Color Changer app and Kitchen Timer app by showing her a Kecleon or Snorlax respectively. She has an unused script to give the player the Alarm Clock app if she is shown a Loudred, and the Stopwatch app if she is shown a Voltorb.

The text for this script remains untranslated. Below is my own translation of the text.

Alarm Clock

Japanese	English
えーっとね…… あしを　ふみならして おおごえを　だしてる　ポケモン！	Let me see... A Pokémon that stomps its feet and shouts loudly!
あら！　ドゴーム！　すてき！ あたしも　ドゴームを　モチーフにした ポケッチアプリ　もってるの！ みせてくれた　おれいに　あげるね！	Oh! A LOUDRED! How lovely! I have a Pokétch app that has a LOUDRED motif. You can have it for showing me a real LOUDRED!

Stopwatch

Japanese	English
えーっとね…… モンスターボールみたいで そうじゃない　ポケモン！	Let me see... A Pokémon that looks like a Poké Ball but isn't one!
あら！　ビリリダマ！　しびれる！ あたしも　ビリリダマを　あしらった ポケッチアプリ　もってるの！ みせてくれた　おれいに　あげるね！	Oh! A VOLTORB! I'm tingling! I have a Pokétch app that features a VOLTORB design. You can have it for showing me a real VOLTORB!

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Sudowoodo Sound

From 2006/06/23 build
The very last sound effect is called SE-USSOKI (Sudowoodo's Japanese name). As expected, it plays a sound of Sudowoodo shaking, similar to the one that appears in GSC and RSE. However, there is no Sudowoodo event in Diamond/Pearl. It can only be found in the tall grass. It is unknown where it would have appeared in the overworld if at all, but one theory is that it may have been on Route 210 in place of the Psyduck. Bonsly can also be found on that route.

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Diamond/Pearl Battle Factory

There are many mentions of a Battle Factory in Diamond/Pearl's source code, but the Battle Factory would not appear until Platinum.
Other than the Battle Tower, it is the only battle facility of the Battle Frontier that appears here.

There is also a BGM track called BF-FACT, which likely stands for Battle Frontier Factory, but it is the same as the Gym theme.

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I tried playing through beta DP

I played the 2006/06/23 build like a normal game, and these are some things I found.

If you have a save file, you can see go to Mystery Gift from the menu like normal, and you already have a Wonder Card! But it's just a jumbled mess of letters, and it's from December 31, 2099. On the bright side, apparently we can send this Mystery Gift to 9 other people!

There's a Happiny Egg you can get in Hearthome City, just like in the final game, but here, you can also put it in the Day-Care. The Day-Care lady will accept it like a normal Pokémon, and even say the name of the Pokémon inside the Egg. Interestingly, if you have the Day-Care Pokétch App, you can view the Egg's status and see that it starts at Level 5 instead of Level 1, which means they hadn't yet changed the Egg hatching level from Gen III. (Sorry the Egg in my picture is higher leveled. I've been walking around a lot.) By the way, don't view your Egg's summary screen because it will crash the game.

There's also one more Egg-related crash I found. If you take your Egg out of the Day-Care, you might get this (second image). From the error message, it's probably related to Moves (Moves are called Waza in Japanese). You can take your Egg out of the Day-Care just fine if it's immediately after putting it in, but if it's leveled up enough to learn some moves, the game will crash upon giving you the Egg.

You can take your Pokémon for a walk in Amity Square like normal. I brought my Psyduck along! However, when you leave Amity Square, the game will still think you have a Pokémon following you, and won't allow you to do things like ride a Bike. The game will tell you "You can't use this with someone following you!" Even if you restart the game, you'll still stuck like this. The biggest issue with this is that if you go into the tall grass in this state, the game will crash.

I assume what's happening is that since you're still in follower mode, the game expects there to be another trainer with you to do a multi battle with, but since there's no actual trainer there, the game crashes. This seems to only happen if you've never had a follower (like Cheryl, Mira, etc.) before and your Pokémon is your first one. If you have had a trainer following you before, the game will use your previous follower. If you get stuck with your Pokémon being the only follower you've had, go get a real one like Cheryl and have her leave. She will replace your Pokémon and then you should be back to normal.

Wild double battles don't seem to work correctly. Usually, you'll have to faint one Pokémon before you can catch the other. Here, you can throw a Poké Ball at any time, but it will always catch the Pokémon on the right. Even if the Pokémon on the right has fainted, you will catch the fainted Pokémon and never the one on the left.

Also, one really small thing I found interesting is that even though some of the Balls don't have bag icons, they already have throwing sprites. Maybe this means they worked on those before making the bag sprites.

If you talk to one of the Underground Air Vents, they'll turn to face your direction, but they become a glitchy mess since they probably aren't supposed to have turning sprites.

Apparently, you meet Marley (using Buck's sprite) right when you enter Victory Road. You take her to the exit in front of the Pokémon League, and she says she just wanted to see the waterfall. In the final game, she appears in a different part of Victory Road and you take her to Route 224..

The GTS (Global Trade System) is called the GTC (Global Trade Center). The name change may have been because of its similarity to the World Trade Center? The background for connecting to Nintendo WFC is also green instead of blue.

Professor Oak gives you the Alarm Clock Poketch App upon entering Pal Park for the first time.

Wow! Turns out the text for getting the Stopwatch is still being used at this point.

There are maps with "fac" in the name, which may be the Battle Factory? They're grouped in with the Battle Tower maps. Since there was also the BF-FACT track, this might be another piece of evidence of the factory's existence in Diamond/Pearl.